Search results for: sequences of AMR gene

Authors: Joulié Aurélien, Jourdain Elsa, Bailly Xavier, Gasqui Patrick, Yang Elise, Leblond Agnès, Rousset Elodie, Sidi-Boumedine Karim

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Q fever is a worldwide zoonosis caused by the gram-negative obligate intracellular bacterium Coxiella burnetii. Following the recent outbreaks in the Netherlands, a hyper virulent clone was found to be the cause of severe human cases of Q fever. In livestock, Q fever clinical manifestations are mainly abortions. Although the abortion rates differ between ruminant species, C. burnetii’s virulence remains understudied, especially in enzootic areas. In this study, the infectious potential of three C. burnetii isolates collected from French farms of small ruminants were compared to the reference strain Nine Mile (in phase II and in an intermediate phase) using an in vivo (CD1 mice) model. Mice were challenged with 105 live bacteria discriminated by propidium monoazide-qPCR targeting the icd-gene. After footpad inoculation, spleen and popliteal lymph node were harvested at 10 days post-inoculation (p.i). The strain invasiveness in spleen and popliteal nodes was assessed by qPCR assays targeting the icd-gene. Preliminary results showed that the avirulent strains (in phase 2) failed to pass the popliteal barrier and then to colonize the spleen. This model allowed a significant differentiation between strain’s invasiveness on biological host and therefore identifying distinct virulence profiles. In view of these results, we plan to go further by testing fifteen additional C. burnetii isolates from French farms of sheep, goat and cattle by using the above-mentioned in vivo model. All 15 strains display distant MLVA (multiple-locus variable-number of tandem repeat analysis) genotypic profiles. Five of the fifteen isolates will bee also tested in vitro on ovine and bovine macrophage cells. Cells and supernatants will be harvested at day1, day2, day3 and day6 p.i to assess in vitro multiplication kinetics of strains. In conclusion, our findings might help the implementation of surveillance of virulent strains and ultimately allow adapting prophylaxis measures in livestock farms.

Keywords: Q fever, invasiveness, ruminant, virulence

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Authors: Guillaume Soubeyran, Fabrice Micoud, Benoit Morin, Jean-Philippe Poirot-Crouvezier, Magali Reytier

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Proton Exchange Membrane Fuel Cell (PEMFC) technology is considered as a solution for the reduction of CO2 emissions. However, this technology still meets several challenges for high-scale industrialization. In this context, the increase of durability remains a critical aspect for competitiveness of this technology. Fortunately, performance degradations in nominal operating conditions is partially reversible, meaning that if specific conditions are applied, a partial recovery of fuel cell performance can be achieved, while irreversible degradations can only be mitigated. Thus, it is worth studying the optimal conditions to rejuvenate these reversible degradations and assessing the long-term impact of such procedures on the performance of the cell. Reversible degradations consist mainly of anode Pt active sites poisoning by carbon monoxide at the anode, heterogeneities in water management during use, and oxidation/deactivation of Pt active sites at the cathode. The latter is identified as a major source of reversible performance loss caused by the presence oxygen, high temperature and high cathode potential that favor platinum oxidation, especially in high efficiency operating points. Hence, we studied here a recovery procedure aiming at reducing the platinum oxides by decreasing cathode potential during operation. Indeed, the application of short air starvation phase leads to a drop of cathode potential. Cell performances are temporarily increased afterwards. Nevertheless, local temperature and current heterogeneities within the cells are favored and shall be minimized. The consumption of fuel during the recovery phase shall also be considered to evaluate the global efficiency. Consequently, the purpose of this work is to find an optimal compromise between the recovery of reversible degradations by air starvation, the increase of global cell efficiency and the mitigation of irreversible degradations effects. Different operating parameters have first been studied such as cell voltage, temperature and humidity in single cell set-up. Considering the global PEMFC system efficiency, tests showed that reducing duration of recovery phase and reducing cell voltage was the key to ensure an efficient recovery. Recovery phase frequency was a major factor as well. A specific method was established to find the optimal frequency depending on the duration and voltage of the recovery phase. Then, long-term degradations have also been studied by applying FC-DLC cycles based on NEDC cycles on a 4-cell short stack by alternating test sequences with and without recovery phases. Depending on recovery phase timing, cell efficiency during the cycle was increased up to 2% thanks to a mean voltage increase of 10 mV during test sequences with recovery phases. However, cyclic voltammetry tests results suggest that the implementation of recovery phases causes an acceleration of the decrease of platinum active areas that could be due to the high potential variations applied to the cathode electrode during operation.

Keywords: durability, PEMFC, recovery procedure, reversible degradation

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Authors: Hanaa M. Abu El Einin, Ahmed T. Sharaf El- Din

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Biomphalaria snails play an integral role in the transmission of Schistosoma mansoni, the causative agent for human schistosomiasis. Two species of Biomphalaria were reported from Egypt, Biomphalaria alexandrina and Biomphalaria glabrata, and later on a hybrid of B. alexandrina and B. glabrata was reported in streams at Nile Delta. All were known to be excellent hosts of S. mansoni. Host-parasite relationship can be viewed in terms of snail susceptibility and parasite infectivity. The objective of this study will highlight the progress that has been made in using molecular approaches to describe the correct identification of snail species that participating in transmission of schistosomiasis, rapid diagnose of infection in addition to susceptibility and resistance type. Snails were identified using of molecular methods involving Randomly Amplified Polymorphic DNA (RAPD), Polymerase Chain Reaction, Restriction Fragment Length Polymorphisms (PCR-RFLP) and Species - specific- PCR. Molecular approaches to diagnose parasite in snails from Egypt: Nested PCR assay and small subunit (SSU) rRNA gene. Also RAPD PCR for study susceptible and resistance phenotype. The results showed that RAPD- PCR, PCR-RFLP and species-specific-PCR techniques were confirmed that: no evidence for the presence of B. glabrata in Egypt, All Biomphalaria snails collected identified as B. alexandrina snail i-e B alexandrinia is a common and no evidence for hybridization with B. glabrata. The adopted specific nested PCR assay revealed much higher sensitivity which enables the detection of S. mansoni infected snails down to 3 days post infection. Nested PCR method for detection of infected snails using S. mansoni fructose -1,6- bisphosphate aldolase (SMALDO) primer, these primers are specific only for S. mansoni and not cross reactive with other schistosomes or molluscan aldolases Nested PCR for such gene is sensitive enough to detect one cercariae. Genetic variations between B. alexandrina strains that are susceptible and resistant to Schistosoma infec¬tion using a RAPD-PCR showed that 39.8% of the examined snails collected from the field were resistant, while 60.2% of these snails showed high infection rates. In conclusion the genetics of the intermediate host plays a more important role in the epidemiological control of schistosomiasis.

Keywords: biomphalaria, molecular differentiation, parasite detection, schistosomiasis

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Authors: Prince Vivek, Vijay K. Bharti, Manishi Mukesh, Ankita Sharma, Om Prakash Chaurasia, Bhuvnesh Kumar

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High performance of endurance in equid requires adaptive changes involving physio-biochemical, and molecular responses in an attempt to regain homeostasis. We hypothesized that the identification of the suitable reference genes might be considered for assessing of endurance related traits in pony at high altitude and may ensure for individuals struggling to potent endurance trait in ponies at high altitude. A total of 12 mares of ponies, Zanskar breed, were divided into three groups, group-A (without load), group-B, (60 Kg) and group-C (80 Kg) on backpack loads were subjected to a load carry protocol, on a steep climb of 4 km uphill, and of gravel, uneven rocky surface track at an altitude of 3292 m to 3500 m (endpoint). Blood was collected before and immediately after the load carry on sodium heparin anticoagulant, and the peripheral blood mononuclear cell was separated for total RNA isolation and thereafter cDNA synthesis. Real time-PCR reactions were carried out to evaluate the mRNAs expression profile of a panel of putative internal control genes (ICGs), related to different functional classes, namely glyceraldehyde 3-phosphate dehydrogenase (GAPDH), β₂ microglobulin (β₂M), β-actin (ACTB), ribosomal protein 18 (RS18), hypoxanthine-guanine phosophoribosyltransferase (HPRT), ubiquitin B (UBB), ribosomal protein L32 (RPL32), transferrin receptor protein (TFRC), succinate dehydrogenase complex subunit A (SDHA) for normalizing the real-time quantitative polymerase chain reaction (qPCR) data of native pony’s. Three different algorithms, geNorm, NormFinder, and BestKeeper software, were used to evaluate the stability of reference genes. The result showed that GAPDH was best stable gene and stability value for the best combination of two genes was observed TFRC and β₂M. In conclusion, the geometric mean of GAPDH, TFRC and β₂M might be used for accurate normalization of transcriptional data for assessing endurance related traits in Zanskar ponies during load carrying.

Keywords: endurance exercise, ubiquitin B (UBB), β₂ microglobulin (β₂M), high altitude, Zanskar ponies, reference gene

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Authors: Louise H. Gracioso, Marcela P.G. Baltazar, Ingrid R. Avanzi, Bruno Karolski, Luciana J. Gimenes, Claudio O. Nascimento, Elen A. Perpetuo

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Introduction: Higher copper concentrations promote a selection pressure on organisms such as plants, fungi and bacteria, which allows surviving only the resistant organisms to the contaminated site. This selective pressure keeps only the organisms most resistant to a specific condition and subsequently increases their bioremediation potential. Despite the bacteria importance for biosphere maintenance, it is estimated that only a small fraction living microbial species has been described and characterized. Due to the molecular biology development, tools based on analysis 16S ribosomal RNA or another specific gene are making a new scenario for the characterization studies and identification of microorganisms in the environment. News identification of microorganisms methods have also emerged like Biotyper (MALDI / TOF), this method mass spectrometry is subject to the recognition of spectroscopic patterns of conserved and features proteins for different microbial species. In view of this, this study aimed to isolate bacteria resistant to copper present in a Copper Processing Area (Sossego Mine, Canaan, PA) and identifies them in two different methods: Recent (spectrometry mass) and conventional. This work aimed to use them for a future bioremediation of this Mining. Material and Methods: Samples were collected at fifteen different sites of five periods of times. Microorganisms were isolated from mining wastes by culture enrichment technique; this procedure was repeated 4 times. The isolates were inoculated into MJS medium containing different concentrations of chloride copper (1mM, 2.5mM, 5mM, 7.5mM and 10 mM) and incubated in plates for 72 h at 28 ºC. These isolates were subjected to mass spectrometry identification methods (Biotyper – MALDI/TOF) and 16S gene sequencing. Results: A total of 105 strains were isolated in this area, bacterial identification by mass spectrometry method (MALDI/TOF) achieved 74% agreement with the conventional identification method (16S), 31% have been unsuccessful in MALDI-TOF and 2% did not obtain identification sequence the 16S. These results show that Biotyper can be a very useful tool in the identification of bacteria isolated from environmental samples, since it has a better value for money (cheap and simple sample preparation and MALDI plates are reusable). Furthermore, this technique is more rentable because it saves time and has a high performance (the mass spectra are compared to the database and it takes less than 2 minutes per sample).

Keywords: copper mining area, bioremediation, microorganisms, identification, MALDI/TOF, RNA 16S

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Authors: Gyu-Dong Kim, Wuk-Jae Yoo, Sang-Youl Lee

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Composite structures offer numerous advantages over conventional structural systems in the form of higher specific stiffness and strength, lower life-cycle costs, and benefits such as easy installation and improved safety. Recently, there has been a considerable increase in the use of composites in engineering applications and as wraps for seismic upgrading and repairs. However, these composites deteriorate with time because of outdated materials, excessive use, repetitive loading, climatic conditions, manufacturing errors, and deficiencies in inspection methods. In particular, damaged fibers in a composite result in significant degradation of structural performance. In order to reduce the failure probability of composites in service, techniques to assess the condition of the composites to prevent continual growth of fiber damage are required. Condition assessment technology and nondestructive evaluation (NDE) techniques have provided various solutions for the safety of structures by means of detecting damage or defects from static or dynamic responses induced by external loading. A variety of techniques based on detecting the changes in static or dynamic behavior of isotropic structures has been developed in the last two decades. These methods, based on analytical approaches, are limited in their capabilities in dealing with complex systems, primarily because of their limitations in handling different loading and boundary conditions. Recently, investigators have introduced direct search methods based on metaheuristics techniques and artificial intelligence, such as genetic algorithms (GA), simulated annealing (SA) methods, and neural networks (NN), and have promisingly applied these methods to the field of structural identification. Among them, GAs attract our attention because they do not require a considerable amount of data in advance in dealing with complex problems and can make a global solution search possible as opposed to classical gradient-based optimization techniques. In this study, we propose an alternative damage-detection technique that can determine the degraded stiffness distribution of vibrating laminated composites made of Glass Fiber-reinforced Polymer (GFRP). The proposed method uses a modified form of the bivariate Gaussian distribution function to detect degraded stiffness characteristics. In addition, this study presents a method to detect the fiber property variation of laminated composite plates from the micromechanical point of view. The finite element model is used to study free vibrations of laminated composite plates for fiber stiffness degradation. In order to solve the inverse problem using the combined method, this study uses only first mode shapes in a structure for the measured frequency data. In particular, this study focuses on the effect of the interaction among various parameters, such as fiber angles, layup sequences, and damage distributions, on fiber-stiffness damage detection.

Keywords: stiffness detection, fiber damage, genetic algorithm, layup sequences

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Authors: Passkorn Khanthongthip, John T. Novak

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Many studies have been reported that the nZVI and MgO NPs were often found in waste activated sludge (WAS). However, little is known about the impact of those NPs on WAS stabilization. The aims of this study were to investigate the effects of both NPs on WAS anaerobic digestion for methane production and to examine the change of metanogenic population under those different environments using qPCR. Four dosages (2, 50, 100, and 200 mg/g-TSS) of MgO NPs were added to four different bottles containing WAS to investigate the impact of MgO NPs on methane production during WAS anaerobic digestion. The effects of nZVI on methane production during WAS anaerobic digestion were also conducted in another four bottles using the same methods described above except that the MgO NPs were replaced by nZVI. A bottle of WAS anaerobic digestion without nanoparticles addition was also operated to serve as a control. It was found that the relative amounts, compared to the control system, of methane production in each WAS anaerobic digestion bottle adding 2, 50, 100, 200 mg/gTSS MgO NPs were 98, 62, 28, and 14 %, respectively. This suggests that higher MgO NPs resulted in lower methane production. The data of batch test for the effects of corresponding released Mg2+ indicated that 50 mg/gTSS MgO NPs or higher could inhibit methane production at least 25%. Moreover, the volatile fatty acid (VFA) concentration was 328, 384, 928, 3,684, and 7,848 mg/L for the control and four WAS anaerobic digestion bottles with 2, 50, 100, 200 mg/gTSS MgO NPs addition, respectively. Higher VFA concentration could reduce pH and subsequently decrease methanogen growth, resulting in lower methane production. The relative numbers of total gene copies of methanogens analyzed from samples taken from WAS anaerobic digestion bottles were approximately 99, 68, 38, and 24 % of control for the addition of 2, 50, 100, and 200 mg/gTSS, respectively. Obviously, the more MgO NPs appeared in sludge anaerobic digestion system, the less methanogens remained. In contrast, the relative amount of methane production found in another four WAS anaerobic digestion bottles adding 2, 50, 100, and 200 mg/gTSS nZVI were 102, 128, 112, and 104 % of the control, respectively. The measurement of methanogenic population indicated that the relative content of methanogen gene copies were 101, 132, 120, and 112 % of those found in control, respectively. Additionally, the cumulative VFA was 320, 234, 308, and 330 mg/L, respectively. This reveals that nZVI addition could assist to increase methanogenic population. Higher amount of methanogen accelerated VFA degradation for greater methane production, resulting in lower VFA accumulation in digesters. Moreover, the data for effects of corresponding released Fe2+ conducted by batch tests suggest that the addition of approximately 50 mg/gTSS nZVI increased methane production by 20%. In conclusion, the presence of MgO NPs appeared to diminish the methane production during WAS anaerobic digestion. Higher MgO NPs dosages resulted in more inhibition on methane production. In contrast, nZVI addition promoted the amount of methanogenic population which facilitated methane production.

Keywords: magnesium oxide nanoparticles, methane production, methanogenic population, nano zerovalent iron

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Authors: Samantha A. Cintron, Janet Pierce, Mihaela E. Sardiu, Diane Mahoney, Jill Peltzer, Bhanu Gupta, Qiuhua Shen

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High output heart failure (HOHF) is characterized a high output state resulting from an underlying disease process and is commonly caused by obesity. As obesity levels increase, more individuals will be at risk for obesity-related HOHF. However, the underlying pathophysiologic mechanisms of obesity-related HOHF are not well understood and need further research. The aim of the study was to describe the differences in leukocyte transcriptomes of morbidly obese patients with HOHF and those with non-HOHF. In this cross-sectional study, the study team collected blood samples, demographics, and clinical data of six patients with morbid obesity and HOHF and six patients with morbid obesity and non-HOHF. The study team isolated the peripheral blood leukocyte RNA and applied stranded total RNA sequencing. Differential gene expression was calculated, and Ingenuity Pathway Analysis software was used to interpret the canonical pathways, functional changes, upstream regulators, and mechanistic and causal networks that were associated with the significantly different leukocyte transcriptomes. The study team identified 116 differentially expressed genes; 114 were upregulated, and 2 were downregulated in the HOHF group (Benjamini-Hochberg adjusted p-value ≤ 0.05 and log2(fold-change) of ±1). The differentially expressed genes were involved with cell proliferation, mitochondrial function, erythropoiesis, erythrocyte stability, and apoptosis. The top upregulated canonical pathways associated with differentially expressed genes were autophagy, adenosine monophosphate-activated protein kinase signaling, and senescence pathways. Upstream regulator GATA Binding Protein 1 (GATA1) and a network associated with nuclear factor kappa-light chain-enhancer of activated B cells (NF-kB) were also identified based on the different leukocyte transcriptomes of morbidly obese patients with HOHF and non-HOHF. To the author’s best knowledge, this is the first study that reported the differential gene expression in patients with obesity-related HOHF and demonstrated the unique pathophysiologic mechanisms underlying the disease. Further research is needed to determine the role of cellular function and maintenance, inflammation, and iron homeostasis in obesity-related HOHF.

Keywords: cardiac output, heart failure, obesity, transcriptomics

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Authors: Vaishnavi Shivde, Shrishti Sinha, Trapti Mishra

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Traffic light detection from a moving vehicle is an important technology both for driver safety assistance functions as well as for autonomous driving in the city. This paper proposed a deep-learning-based traffic light recognition method that consists of a pixel-wise image segmentation technique and a fully convolutional network i.e., UNET architecture. This paper has used a method for detecting the position and recognizing the state of the traffic lights in video sequences is presented and evaluated using Traffic Light Dataset which contains masked traffic light image data. The first stage is the detection, which is accomplished through image processing (image segmentation) techniques such as image cropping, color transformation, segmentation of possible traffic lights. The second stage is the recognition, which means identifying the color of the traffic light or knowing the state of traffic light which is achieved by using a Convolutional Neural Network (UNET architecture).

Keywords: traffic light detection, image segmentation, machine learning, classification, convolutional neural networks

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Authors: Hamsa T. Tayeb, Mohammad A. Arafah, Dana M. Bakheet, Duaa M. Khalaf, Agnieszka Tarnoska, Nduna Dzimiri

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Background: CYP2D6 is a member of the cytochrome P450 mixed-function oxidase system. The enzyme is responsible for the metabolism and elimination of approximately 25% of clinically used drugs, especially in breast cancer and psychiatric therapy. Different phenotypes have been described displaying alleles that lead to a complete loss of enzyme activity, reduced function (poor metabolizers – PM), hyperfunctionality (ultrarapid metabolizers–UM) and therefore drug intoxication or loss of drug effect. The prevalence of these variants may vary among different ethnic groups. Furthermore, the xTAG system has been developed to categorized all patients into different groups based on their CYP2D6 substrate metabolization. Aim of the study: To determine the prevalence of the different CYP2D6 variants in our population, and to evaluate their clinical relevance in personalized medicine. Methodology: We used the Luminex xMAP genotyping system to sequence 305 Saudi individuals visiting the Blood Bank of our Institution and determine which polymorphisms of CYP2D6 gene are prevalent in our region. Results: xTAG genotyping showed that 36.72% (112 out of 305 individuals) carried the CYP2D6_*2. Out of the 112 individuals with the *2 SNP, 6.23% had multiple copies of *2 SNP (19 individuals out of 305 individuals), resulting in an UM phenotype. About 33.44% carried the CYP2D6_*41, which leads to decreased activity of the CYP2D6 enzyme. 19.67% had the wild-type alleles and thus had normal enzyme function. Furthermore, 15.74% carried the CYP2D6_*4, which is the most common nonfunctional form of the CYP2D6 enzyme worldwide. 6.56% carried the CYP2D6_*17, resulting in decreased enzyme activity. Approximately 5.73% carried the CYP2D6_*10, consequently decreasing the enzyme activity, resulting in a PM phenotype. 2.30% carried the CYP2D6_*29, leading to decreased metabolic activity of the enzyme, and 2.30% carried the CYP2D6_*35, resulting in an UM phenotype, 1.64% had a whole-gene deletion CYP2D6_*5, thus resulting in the loss of CYP2D6 enzyme production, 0.66% carried the CYP2D6_*6 variant. One individual carried the CYP2D6_*3(B), producing an inactive form of the enzyme, which leads to decrease of enzyme activity, resulting in a PM phenotype. Finally, one individual carried the CYP2D6_*9, which decreases the enzyme activity. Conclusions: Our study demonstrates that different CYP2D6 variants are highly prevalent in ethnic Saudi Arabs. This finding sets a basis for informed genotyping for these variants in personalized medicine. The study also suggests that xTAG is an appropriate procedure for genotyping the CYP2D6 variants in personalized medicine.

Keywords: CYP2D6, hormonal breast cancer, pharmacogenetics, polymorphism, psychiatric treatment, Saudi population

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Authors: Nuha Mansour Alhazmi, Magda Mohamed Aly, Fardus M. Bokhari, Ahmed Bahieldin, Sherif Edris

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Out of 30 fungal isolates, 2 new isolates were proven to degrade poly-β-hydroxybutyrate (PHB). Enzyme assay for these isolates indicated the optimal environmental conditions required for depolymerase enzyme to induce the highest level of biopolymer degradation. The two isolates were basically characterized at the morphological level as Trichoderma asperellum (isolate S1), and Aspergillus fumigates (isolate S2) using standard approaches. The aim of the present study was to characterize these two isolates at the molecular level based on the highly diverged rRNA gene(s). Within this gene, two domains of the ribosome large subunit (LSU) namely internal transcribed spacer (ITS) and 26S were utilized in the analysis. The first domain comprises the ITS1/5.8S/ITS2 regions ( > 500 bp), while the second domain comprises the D1/D2/D3 regions ( > 1200 bp). Sanger sequencing was conducted at Macrogen (Inc.) for the two isolates using primers ITS1/ITS4 for the first domain, while primers LROR/LR7 for the second domain. Sizes of the first domain ranged between 594-602 bp for S1 isolate and 581-594 bp for S2 isolate, while those of the second domain ranged between 1228-1238 bp for S1 isolate and 1156-1291 for S2 isolate. BLAST analysis indicated 99% identities of the first domain of S1 isolate with T. asperellum isolates XP22 (ID: KX664456.1), CTCCSJ-G-HB40564 (ID: KY750349.1), CTCCSJ-F-ZY40590 (ID: KY750362.1) and TV (ID: KU341015.1). BLAST of the first domain of S2 isolate indicated 100% identities with A. fumigatus isolate YNCA0338 (ID: KP068684.1) and strain MEF-Cr-6 (ID: KU597198.1), while 99% identities with A. fumigatus isolate CCA101 (ID: KT877346.1) and strain CD1621 (ID: JX092088.1). Large numbers of other T. asperellum and A. fumigatus isolates and strains showed high level of identities with S1 and S2 isolates, respectively, based on the diversity of the first domain. BLAST of the second domain of S1 isolate indicated 99 and 100% identities with only two strains of T. asperellum namely TR 3 (ID: HM466685.1) and G (ID: KF723005.1), respectively. However, other T. species (ex., atroviride, hamatum, deliquescens, harzianum, etc.) also showed high level of identities. BLAST of the second domain of S2 isolate indicated 100% identities with A. fumigatus isolate YNCA0338 (ID: KP068684.1) and strain MEF-Cr-6 (ID: KU597198.1), while 99% identities with A. fumigatus isolate CCA101 (ID: KT877346.1) and strain CD1621 (ID: JX092088.1). Large numbers of other A. fumigatus isolates and strains showed high level of identities with S2 isolate. Overall, the results of molecular characterization based on rRNA diversity for the two isolates of T. asperellum and A. fumigatus matched those obtained by morphological characterization. In addition, ITS domain proved to be more sensitive than 26S domain in diversity profiling of fungi at the species level.

Keywords: Aspergillus fumigates, Trichoderma asperellum, PHB, degradation, BLAST, ITS, 26S, rRNA

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Authors: Yazhi Huang, Jing Yang, Dingge Ying, Yan Zhang, Vorasuk Shotelersuk, Nattiya Hirankarn, Pak Chung Sham, Yu Lung Lau, Wanling Yang

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Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT.

Keywords: human leukocyte antigens, next generation sequencing, whole exome sequencing, HLA typing

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Authors: M. Bhattarai, B. B. Rana, M. Kamimukai, I. Takamure, T. Kawano, M. Murai

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The sd1-d allele at the sd1 locus on chromosome 1, originating from Taiwanese variety Dee-geo-woo-gen, has been playing important role for developing short-culm and lodging-resistant indica varieties such as IR36 in rice. The dominant allele SD1 for long culm at the locus is differentiated into SD1-in and SD1-ja which are harbored in indica and japonica subspecies’s, respectively. The sd1-d of an indica variety IR36 was substituted with SD1-in or SD1-ja by recurrent backcrosses of 17 times with IR36, and two isogenic tall lines regarding the respective dominant alleles were developed by using an indica variety IR5867 and a japonica one ‘Koshihikari’ as donors, which were denoted by '5867-36' and 'Koshi-36', respectively. The present study was conducted to examine the effect of sd1-d on yield and related traits as compared with SD1-in and SD1-ja, by using the two isogenic tall lines. Seedlings of IR36 and the two isogenic lines were transplanted on an experimental field of Kochi University, by the planting distance of 30 cm × 15 cm with two seedlings per hill, on May 3, 2017. Chemical fertilizers were supplied by basal application and top-dressing at a rate of 8.00, 6.57 and 7.52 g/m², respectively, for N, P₂O₅ and K₂O in total. Yield, yield components, and other traits were measured. Culm length (cm) was in the order of 5867-36 (101.9) > Koshi-36 (80.1) > IR36 (60.0), where '>' indicates statistically significant difference at the 5% level. Accordingly, sd1-d reduced culm by 41.9 and 20.1 cm, compared with SD1-in and SD1-ja, respectively, and the effect of elongating culm was higher in the former allele than in the latter one. Total brown rice yield (g/m²), including unripened grains, was in the order of IR36 (611) ≧ 5867-36 (586) ≧ Koshi-36 (572), indicating non-significant differences among them. Yield-1.5mm sieve (g/m²) was in the order of IR36 (596) ≧ 5867-36 (575) ≧ Koshi-36 (558). Spikelet number per panicle was in the order of 5867-36 (89.2) ≧ IR36 (84.7) ≧ Koshi-36 (79.8), and 5867-36 > Koshi-36. Panicle number per m² was in the order of IR36 (428) ≧ Koshi-36 (403) ≧ 5867-36 (353), and IR36 > 5867-36, suggesting that sd1-d increased number of panicles compared with SD1-in. Ripened-grain percentage-1.5mm sieve was in the order of Koshi-36 (86.0) ≧ 5867-36 (85.0) ≧ IR36 (82.7), and Koshi-36 > IR36. Thousand brown-rice-grain weight-1.5mm sieve (g) was in the order of 5867-36 (21.5) > Koshi-36 (20.2) ≧ IR36 (19.9). Total dry weight at maturity (g/m²) was in the order of 5867-36 (1404 ) ≧ IR36 (1310) ≧ Kosihi-36 (1290). Harvest index of total brown rice (%) was in the order of IR36 (39.6) > Koshi-36 (37.7) > 5867-36 (35.5). Hence, sd1-d did not exert significant effect on yield in indica genetic background. However, lodging was observed from the late stage of maturity in 5867-36 and Koshi-36, particularly in the former, which was principally due to their long culms. Consequently, sd1-d enables higher yield with higher fertilizer application, by enhancing lodging resistance, particularly in indica subspecies.

Keywords: rice, dwarfing gene, sd1-d, SD1-in, SD1-ja, yield

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Authors: Watchara Songserm, Teeradej Wuttipornpun

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This paper presents a genetic algorithm based permutation and non-permutation scheduling heuristics (GAPNP) to solve a multi-stage finite capacity material requirement planning (FCMRP) problem in automotive assembly flow shop with unrelated parallel machines. In the algorithm, the sequences of orders are iteratively improved by the GA characteristics, whereas the required operations are scheduled based on the presented permutation and non-permutation heuristics. Finally, a linear programming is applied to minimize the total cost. The presented GAPNP algorithm is evaluated by using real datasets from automotive companies. The required parameters for GAPNP are intently tuned to obtain a common parameter setting for all case studies. The results show that GAPNP significantly outperforms the benchmark algorithm about 30% on average.

Keywords: capacitated MRP, genetic algorithm, linear programming, automotive industries, flow shop, application in industry

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Authors: Fatima Arrutia, Francisco Amador Riera

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The meat industry generates large volumes of blood as a result of meat processing. Several industrial procedures have been implemented in order to treat this by-product, but are focused on the production of low-value products, and in many cases, blood is simply discarded as waste. Besides, in addition to economic interests, there is an environmental concern due to bloodborne pathogens and other chemical contaminants found in blood. Consequently, there is a dire need to find extensive uses for blood that can be both applicable to industrial scale and able to yield high value-added products. Blood has been recognized as an important source of protein. The main blood serum protein in mammals is serum albumin. One of the top trends in food market is functional foods. Among them, bioactive peptides can be obtained from protein sources by microbiological fermentation or enzymatic and chemical hydrolysis. Bioactive peptides are short amino acid sequences that can have a positive impact on health when administered. The main drawback for bioactive peptide production is the high cost of the isolation, purification and characterization techniques (such as chromatography and mass spectrometry) that make unaffordable the scale-up. On the other hand, membrane technologies are very suitable to apply to the industry because they offer a very easy scale-up and are low-cost technologies, compared to other traditional separation methods. In this work, the possibility of obtaining bioactive peptide fractions from serum albumin by means of a simple procedure of only 2 steps (hydrolysis and membrane filtration) was evaluated, as an exploratory study for possible industrial application. The methodology used in this work was, firstly, a tryptic hydrolysis of serum albumin in order to release the peptides from the protein. The protein was previously subjected to a thermal treatment in order to enhance the enzyme cleavage and thus the peptide yield. Then, the obtained hydrolysate was filtered through a nanofiltration/ultrafiltration flat rig at three different pH values with two different membrane materials, so as to compare membrane performance. The corresponding permeates were analyzed by liquid chromatography-tandem mass spectrometry technology in order to obtain the peptide sequences present in each permeate. Finally, different concentrations of every permeate were evaluated for their in vitro antihypertensive and antioxidant activities though ACE-inhibition and DPPH radical scavenging tests. The hydrolysis process with the previous thermal treatment allowed achieving a degree of hydrolysis of the 49.66% of the maximum possible. It was found that peptides were best transmitted to the permeate stream at pH values that corresponded to their isoelectric points. Best selectivity between peptide groups was achieved at basic pH values. Differences in peptide content were found between membranes and also between pH values for the same membrane. The antioxidant activity of all permeates was high compared with the control only for the highest dose. However, antihypertensive activity was best for intermediate concentrations, rather than higher or lower doses. Therefore, although differences between them, all permeates were promising regarding antihypertensive and antioxidant properties.

Keywords: bioactive peptides, bovine serum albumin, hydrolysis, membrane filtration

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Authors: K. Suresh, R. Arunkumar

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The objective of this study is to investigate the preparation of gramine nano suspension and protective effect of Gramine on the apoptosis of laryngeal cancer cells cell line (HEp-2 and KB). The growth inhibition rate of Hep-2 and KB cells in vitro were measured by MTT assay and apoptosis by, levels of reactive oxygen species, mitochondrial membrane potential, morphological changes and flowcytometry. Based on the results, we determined the effective doses of gramine as 127.23µm/ml for 24 hr and 119.81 µm/ml for 48hr in hep-2 cell line and 147.58 µm ml for 24 hr and 123.74µm µm/ml for 48hr in KB cell line. cytotoxicity effects of gramine were confirmed by treatment of HEp-2 cell and KB cell with IC50 concentration of gramine resulted in sequences of events marked by the enhance the apoptosis accompanied by loss of cell viability, modulation of reactive oxygen species and cell cycle arrest through the induction of G0/G1 phase arrest on HEp-2 cells. Our study suggests that the nanosuspension of gramine possesses the more cytotoxic effect of cancer cells and a novel candidate for cancer chemoprevention.

Keywords: apoptosis, HEp-2 cell line, KB cell line mitochondria, gramine, nanosuspension

Procedia PDF Downloads 447

Authors: Eun-Young Kwon, Myung-Sook Choi, Su-Jung Cho, Ji-Young Choi, So Young Kim, Youngji Han

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Overweight and obesity have been linked to a low-grade chronic inflammatory response and an increased risk of developing metabolic syndrome including insulin resistance, type 2 diabetes mellitus and certain types of cancers. Luteolin is a dietary flavonoid with anti-inflammatory, anti-oxidant, anti-cancer and anti-diabetic properties. However, little is known about the detailed mechanism associated with the effect of luteolin on inflammation-related obesity and its complications. The aim of the present study was to reveal the anti-diabetic effect of luteolin in diet-induced obesity mice using “transcriptomics” tool. Thirty-nine male C57BL/6J mice (4-week-old) were randomly divided into 3 groups and were fed normal diet, high-fat diet (HFD, 20% fat) and HFD+0.005% (w/w) luteolin for 16 weeks. Luteolin improved insulin resistance, as measured by HOMA-IR and glucose tolerance, along with preservation action of pancreatic β-cells, compared to the HFD group. Luteoiln was significantly decreased the levels of leptin and ghrelin that play a pivotal role in energy balance, and the macrophage low-grade inflammation marker sCD163 (soluble Cd antigen 163) in plasma. Activities of hepatic anti-oxidant enzymes (catalase and glutathione peroxidase) were increased, while the levels of plasma transaminase (GOT and GPT) and oxidative damage markers (hepatic mitochondria H2O2 and TBARS) were markedly decreased by luteolin supplementation. In addition, luteolin increased oxidative capacity and fatty acid utilization by presenting decrease in enzyme activities of citrate synthase, cytochrome C oxidase and β-hydroxyacyl CoA dehydrogenase and UCP3 gene expression compared to high-fat diet. Moreover, our microarray results of muscle also revealed down-regulated gene expressions associated with TCA cycle by HFD were reversed to normal level by luteolin treatment. Taken together, our results indicate that luteolin is one of bioactive components for improving insulin resistance by increasing oxidative capacity, modulating anti-oxidant metabolism and suppressing inflammatory signaling cascades in diet-induced obese mice. These results provide possible therapeutic targets for prevention and treatment of diet-induced obesity and its complications.

Keywords: anti-oxidant metabolism, diabetes, luteolin, oxidative capacity

Procedia PDF Downloads 333

Authors: K. Tejasri, K. Suvarna Vani, S. Prathyusha, S. Ramya

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Proteins are chained sequences of amino acids which are brought together by the peptide bonds. Many varying formations of the chains are possible due to multiple combinations of amino acids and rotation in numerous positions along the chain. Protein structure prediction is one of the crucial goals worked towards by the members of bioinformatics and theoretical chemistry backgrounds. Among the four different structure levels in proteins, we emphasize mainly the secondary level structure. Generally, the secondary protein basically comprises alpha-helix and beta-sheets. Multi-class classification problem of data with disparity is truly a challenge to overcome and has to be addressed for the beta strands. Imbalanced data distribution constitutes a couple of the classes of data having very limited training samples collated with other classes. The secondary structure data is extracted from the protein primary sequence, and the beta-strands are predicted using suitable machine learning algorithms.

Keywords: proteins, secondary structure elements, beta-sheets, beta-strands, alpha-helices, machine learning algorithms

Procedia PDF Downloads 90

Authors: Nam-Kuk Kim, Jin Kim, Soomin Park, Changhee Lee, Mijin Chu, Seong-Hun Lee

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In this study, we conducted whole genome re-sequencing of 10 cultivars originated from five countries including Korea, China, India, Pakistan and Ethiopia with Sesamum indicum (Zhongzho No. 13) genome as a reference. Almost 80% of the whole genome sequences of the reference genome could be covered by sequenced reads. Numerous SNP and InDel were detected by bioinformatic analysis. Among these variants, 266,051 SNPs were identified as unique to countries. Pakistan and Ethiopia had high densities of SNPs compared to other countries. Three main clusters (cluster 1: Korea, cluster 2: Pakistan and India, cluster 3: Ethiopia and China) were recovered by neighbor-joining analysis using all variants. Interestingly, some variants were detected in DGAT1 (diacylglycerol O-acyltransferase 1) and FADS (fatty acid desaturase) genes, which are known to be related with fatty acid synthesis and metabolism. These results can provide useful information to understand the regional characteristics and develop DNA markers for origin discrimination of sesame.

Keywords: Sesamum indicum, NGS, SNP, DNA marker

Procedia PDF Downloads 321

Authors: Abdelsabour G. A. Khaled, Galal A.R. El-Sherbeny, Ahmed M. Hassanein, Gameel M. G. Aly

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Classical methods of identification, based on agronomical characterization, are not always the most accurate way due to the instability of these characteristics under the influence of the different environments. In order to estimate the genetic diversity, molecular markers provided excellent tools. In this study, Genetic variation of nine Egyptian jojoba shrubs was tested using ISSR (inter simple sequences repeats), RAPD (random amplified polymorphic DNA) markers and based on the morphological characterization. The average of the percentage of polymorphism (%P) ranged between 58.17% and 74.07% for ISSR and RAPD markers, respectively. The range of genetic similarity percents among shrubs based on ISSR and RAPD markers were from 82.9 to 97.9% and from 85.5 to 97.8%, respectively. The average of PIC (polymorphism information content) values were 0.19 (ISSR) and 0.24 (RAPD). In the present study, RAPD markers were more efficient than the ISSR markers. Where the RAPD technique exhibited higher marker index (MI) average (1.26) compared to ISSR one (1.11). There was an insignificant correlation between the ISSR and RAPD data (0.076, P > 0.05). The dendrogram constructed by the combined RAPD and ISSR data gave a relatively different clustering pattern.

Keywords: correlation, molecular markers, polymorphism, marker index

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Authors: S. M. Kulkarni, D. S. Bormane, S. L. Nalbalwar

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The rapid development in the technology have dramatic impact on the medical health care field. Medical data base obtained with latest machines like CT Machine, MRI scanner requires large amount of memory storage and also it requires large bandwidth for transmission of data in telemedicine applications. Thus, there is need for video compression. As the database of medical images contain number of frames (slices), hence while coding of these images there is need of motion estimation. Motion estimation finds out movement of objects in an image sequence and gets motion vectors which represents estimated motion of object in the frame. In order to reduce temporal redundancy between successive frames of video sequence, motion compensation is preformed. In this paper three step search (TSS) block matching algorithm is implemented on different types of video sequences. It is shown that three step search algorithm produces better quality performance and less computational time compared with exhaustive full search algorithm.

Keywords: block matching, exhaustive search motion estimation, three step search, video compression

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Authors: Debbarma Asis, Guha Chandan

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Tumor Protein-53 (P53) is one of the tumor suppressor proteins. P53 regulates the cell cycle that conserves stability by preventing genome mutation. It is named so as it runs as 53-kilodalton (kDa) protein on Polyacrylamide gel electrophoresis although the actual mass is 43.7 kDa. Experimental evidence has indicated that P53 cancer mutants loses tumor suppression activity and subsequently gain oncogenic activities to promote tumourigenesis. Tumor-specific DNA has recently been detected in the plasma of breast cancer patients. Detection of tumor-specific genetic materials in cancer patients may provide a unique and valuable tumor marker for diagnosis and prognosis. Commercially available MDA-468 breast cancer cell line was used for the proposed study.

Keywords: tumor protein (P53), cancer mutants, MDA-468, tumor suppressor gene

Procedia PDF Downloads 473

Authors: Keigo Ide, Toru Maruyama, Michihiro Ito, Hiroyuki Fujimura, Yoshikatu Nakano, Shoichiro Suda, Sachiyo Aburatani, Haruko Takeyama

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Understanding environmental system is one of the important tasks. In recent years, conservation of coral environments has been focused for biodiversity issues. The damage of coral reef under environmental impacts has been observed worldwide. However, the casual relationship between damage of coral and environmental impacts has not been clearly understood. On the other hand, structure/diversity of marine bacterial community may be relatively robust under the certain strength of environmental impact. To evaluate the coral environment conditions, it is necessary to investigate relationship between marine bacterial composition in coral reef and environmental factors. In this study, the Time Scale Network Analysis was developed and applied to analyze the marine environmental data for investigating the relationship among coral, bacterial community compositions and environmental factors. Seawater samples were collected fifteen times from November 2014 to May 2016 at two locations, Ishikawabaru and South of Sesoko in Sesoko Island, Okinawa. The physicochemical factors such as temperature, photosynthetic active radiation, dissolved oxygen, turbidity, pH, salinity, chlorophyll, dissolved organic matter and depth were measured at the coral reef area. Metagenome and metatranscriptome in seawater of coral reef were analyzed as the biological factors. Metagenome data was used to clarify marine bacterial community composition. In addition, functional gene composition was estimated from metatranscriptome. For speculating the relationships between physicochemical and biological factors, cross-correlation analysis was applied to time scale data. Even though cross-correlation coefficients usually include the time precedence information, it also included indirect interactions between the variables. To elucidate the direct regulations between both factors, partial correlation coefficients were combined with cross correlation. This analysis was performed against all parameters such as the bacterial composition, the functional gene composition and the physicochemical factors. As the results, time scale network analysis revealed the direct regulation of seawater temperature by photosynthetic active radiation. In addition, concentration of dissolved oxygen regulated the value of chlorophyll. Some reasonable regulatory relationships between environmental factors indicate some part of mechanisms in coral reef area.

Keywords: coral environment, marine microbiology, network analysis, omics data analysis

Procedia PDF Downloads 247

Authors: Qianxi Lv, Junying Liang

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Among the various modes of interpreting, simultaneous interpreting (SI) is regarded as a ‘complex’ and ‘extreme condition’ of cognitive tasks while consecutive interpreters (CI) do not have to share processing capacity between tasks. Given that SI exerts great cognitive demand, it makes sense to posit that the output of SI may be more compromised than that of CI in the linguistic features. The bulk of the research has stressed the varying cognitive demand and processes involved in different modes of interpreting; however, related empirical research is sparse. In keeping with our interest in investigating the quantitative linguistic factors discriminating between SI and CI, the current study seeks to examine the potential lexical simplification, syntactic complexity and sequential organization mechanism with a self-made inter-model corpus of transcribed simultaneous and consecutive interpretation, translated speech and original speech texts with a total running word of 321960. The lexical features are extracted in terms of the lexical density, list head coverage, hapax legomena, and type-token ratio, as well as core vocabulary percentage. Dependency distance, an index for syntactic complexity and reflective of processing demand is employed. Frequency motif is a non-grammatically-bound sequential unit and is also used to visualize the local function distribution of interpreting the output. While SI is generally regarded as multitasking with high cognitive load, our findings evidently show that CI may impose heavier or taxing cognitive resource differently and hence yields more lexically and syntactically simplified output. In addition, the sequential features manifest that SI and CI organize the sequences from the source text in different ways into the output, to minimize the cognitive load respectively. We reasoned the results in the framework that cognitive demand is exerted both on maintaining and coordinating component of Working Memory. On the one hand, the information maintained in CI is inherently larger in volume compared to SI. On the other hand, time constraints directly influence the sentence reformulation process. The temporal pressure from the input in SI makes the interpreters only keep a small chunk of information in the focus of attention. Thus, SI interpreters usually produce the output by largely retaining the source structure so as to relieve the information from the working memory immediately after formulated in the target language. Conversely, CI interpreters receive at least a few sentences before reformulation, when they are more self-paced. CI interpreters may thus tend to retain and generate the information in a way to lessen the demand. In other words, interpreters cope with the high demand in the reformulation phase of CI by generating output with densely distributed function words, more content words of higher frequency values and fewer variations, simpler structures and more frequently used language sequences. We consequently propose a revised effort model based on the result for a better illustration of cognitive demand during both interpreting types.

Keywords: cognitive demand, corpus-based, dependency distance, frequency motif, interpreting types, lexical simplification, sequential units distribution, syntactic complexity

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Authors: Veerle Van Hoeck, Ingrid Somers, Dany Morisset

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Anti-nutritional factors such as non-starch polysaccharides (NSP) are present in viscous cereals used to feed poultry. Therefore, exogenous carbohydrases are commonly added to monogastric feed to degrade these NSP. Our hypothesis is that xylanase not only improves laying hen performance and digestibility but also induces a significant shift in microbial composition within the intestinal tract and, thereby, can cause a prebiotic effect. In this context, a better understanding of whether and how the chicken gut flora can be modulated by xylanase is needed. To do so, in the herein laying hen study, the effects of dietary supplementation of xylanase on performance, digestibility, and cecal microbiome were evaluated. A total of 96 HiSex laying hens was used in this experiment (3 diets and 16 replicates of 2 hens). Xylanase was added to the diets at concentrations of 0, 45,000 (15 g/t XygestTM HT) and 90,000 U/kg (30 g/t Xygest HT). The diets were based on wheat (~55 %), soybean, and sunflower meal. The lowest dosage, 45,000 U/kg, significantly increased average egg weight and improved feed efficiency compared to the control treatment (p < 0.05). Egg quality parameters were significantly improved in the experiment in response to the xylanase addition. For example, during the last 28 days of the trial, the 45,000 U/kg and the 90,000 U/kg treatments exhibited an increase in Haugh units and albumin heights (p < 0.05). Compared with the control, organic matter digestibility and N retention were drastically improved in the 45,000 U/kg treatment group, which implies better nutrient digestibility at this lowest recommended dosage compared to the control (p < 0.05). Furthermore, gross energy and crude fat digestibility were improved significantly for birds fed 90,000 U/kg group compared to the control. Importantly, 16S rRNA gene analysis revealed that xylanase at 45,000 U/kg dosages can exert a prebiotic effect. This conclusion was drawn based on studying the sequence variation in the 16S rRNA gene in order to characterize diverse microbial communities of the cecal content. A significant increase in beneficial bacteria (Lactobacilli spp and Enterococcus casseliflavus) was documented when adding 45,000 U/kg xylanase to the diet of laying hens. In conclusion, dietary supplementation of xylanase, even at the lowest dose of (45,000 U/kg), significantly improved laying hen performance and digestibility. Furthermore, it is generally accepted that a proper bacterial balance between the number of beneficial bacteria and pathogenic bacteria in the intestine is vital for the host. It seems that the xylanase enzyme is able to modulate the laying hen microbiome beneficially and thus exerts a prebiotic effect. This microbiome plasticity in response to the xylanase provides an attractive target for stimulating intestinal health.

Keywords: laying hen, prebiotic, XygestTM HT, xylanase

Procedia PDF Downloads 122

Authors: Pratibha Srivastava, Ayyamperumal Jeyaprakash, Gary Steck

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Exotic, invasive tephritid fruit flies (Diptera: Tephritidae) are a major concern to fruit and vegetable production in the USA. Timely detection and identification of these agricultural pests facilitate the possibility of eradication from newly invaded areas. They spread primarily as larvae in infested fruits carried in commerce or personal baggage. Identification of larval stages to species level is difficult but necessary to determine pest loads and their pathways into the USA. The main focus of this study is the New World genus, Anastrepha. Many of its constituent taxa are pests of major economic importance. This study is significant for national quarantine use, as morphological diagnostics to separate larvae of the various members remain poorly developed. Elongation factor 1 alpha sequences were amplified from Anastrepha fraterculus specimens collected from South America (Ecuador and Peru). Phylogenetic analysis was performed to characterize the Anastrepha fraterculus complex at a molecular level.

Keywords: anastrepha, diptera, elongation factor, fruit fly

Procedia PDF Downloads 200

Authors: Katarzyna Lubecka, Kirsty Flower, Megan Beetch, Lucinda Kurzava, Hannah Buvala, Samer Gawrieh, Suthat Liangpunsakul, Tracy Gonzalez, George McCabe, Naga Chalasani, James M. Flanagan, Barbara Stefanska

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Hepatocellular carcinoma (HCC), the most prevalent type of primary liver cancer, is the second leading cause of cancer death worldwide. Late onset of clinical symptoms in HCC results in late diagnosis and poor disease outcome. Approximately 85% of individuals with HCC have underlying liver cirrhosis. However, not all cirrhotic patients develop cancer. Reliable early detection biomarkers that can distinguish cirrhotic patients who will develop cancer from those who will not are urgently needed and could increase the cure rate from 5% to 80%. We used Illumina-450K microarray to test whether blood DNA, an easily accessible source of DNA, bear site-specific changes in DNA methylation in response to HCC before diagnosis with conventional tools (pre-diagnostic). Top 11 differentially methylated sites were selected for validation by pyrosequencing. The diagnostic potential of the 11 pyrosequenced probes was tested in blood samples from a prospective cohort of cirrhotic patients. We identified 971 differentially methylated CpG sites in pre-diagnostic HCC cases as compared with healthy controls (P < 0.05, paired Wilcoxon test, ICC ≥ 0.5). Nearly 76% of differentially methylated CpG sites showed lower levels of methylation in cases vs. controls (P = 2.973E-11, Wilcoxon test). Classification of the CpG sites according to their location relative to CpG islands and transcription start site revealed that those hypomethylated loci are located in regulatory regions important for gene transcription such as CpG island shores, promoters, and 5’UTR at higher frequency than hypermethylated sites. Among 735 CpG sites hypomethylated in cases vs. controls, 482 sites were assigned to gene coding regions whereas 236 hypermethylated sites corresponded to 160 genes. Bioinformatics analysis using GO, KEGG and DAVID knowledgebase indicate that differentially methylated CpG sites are located in genes associated with functions that are essential for gene transcription, cell adhesion, cell migration, and regulation of signal transduction pathways. Taking into account the magnitude of the difference, statistical significance, location, and consistency across the majority of matched pairs case-control, we selected 11 CpG loci corresponding to 10 genes for further validation by pyrosequencing. We established that methylation of CpG sites within 5 out of those 10 genes distinguish cirrhotic patients who subsequently developed HCC from those who stayed cancer free (cirrhotic controls), demonstrating potential as biomarkers of early detection in populations at risk. The best predictive value was detected for CpGs located within BARD1 (AUC=0.70, asymptotic significance ˂0.01). Using an additive logistic regression model, we further showed that 9 CpG loci within those 5 genes, that were covered in pyrosequenced probes, constitute a panel with high diagnostic accuracy (AUC=0.887; 95% CI:0.80-0.98). The panel was able to distinguish pre-diagnostic cases from cirrhotic controls free of cancer with 88% sensitivity at 70% specificity. Using blood as a minimally invasive material and pyrosequencing as a straightforward quantitative method, the established biomarker panel has high potential to be developed into a routine clinical test after validation in larger cohorts. This study was supported by Showalter Trust, American Cancer Society (IRG#14-190-56), and Purdue Center for Cancer Research (P30 CA023168) granted to BS.

Keywords: biomarker, DNA methylation, early detection, hepatocellular carcinoma

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Authors: Sonia Bedhiaf-Romdhani

Abstract:

The sheep (Ovis aries) was domesticated, approximately 11,000 years ago (YBP), in the Fertile Crescent from Asian Mouflon (Ovis Orientalis). The Northern African (NA) sheep is 7,000 years old, represents a remarkable diversity of sheep populations reared under traditional and low input farming systems (LIFS) over millennia. The majority of small ruminants in developing countries are encountered in low input production systems and the resilience of local communities in rural areas is often linked to the wellbeing of small ruminants. Regardless of the rich biodiversity encountered in sheep ecotypes there are four main sheep breeds in the country with 61,6 and 35.4 percents of Barbarine (fat tail breed) and Queue Fine de l’Ouest (thin tail breed), respectively. Phoenicians introduced the Barbarine sheep from the steppes of Central Asia in the Carthaginian period, 3000 years ago. The Queue Fine de l’Ouest is a thin-tailed meat breed heavily concentrated in the Western and the central semi-arid regions. The Noire de Thibar breed, involving mutton-fine wool producing animals, has been on the verge of extinction, it’s a composite black coated sheep breed found in the northern sub-humid region because of its higher nutritional requirements and non-tolerance of the prevailing harsher condition. The D'Man breed, originated from Morocco, is mainly located in the southern oases of the extreme arid ecosystem. A genetic investigation of Tunisian sheep breeds using a genome-wide scan of approximately 50,000 SNPs was performed. Genetic analysis of relationship between breeds highlighted the genetic differentiation of Noire de Thibar breed from the other local breeds, reflecting the effect of past events of introgression of European gene pool. The Queue Fine de l’Ouest breed showed a genetic heterogeneity and was close to Barbarine. The D'Man breed shared a considerable gene flow with the thin-tailed Queue Fine de l'Ouest breed. Native small ruminants breeds, are capable to be efficiently productive if essential ingredients and coherent breeding schemes are implemented and followed. Assessing the status of genetic variability of native sheep breeds could provide important clues for research and policy makers to devise better strategies for the conservation and management of genetic resources.

Keywords: sheep, farming systems, diversity, SNPs.

Procedia PDF Downloads 141

Authors: Boris Melnikov, Ye Zhang, Dmitrii Chaikovskii

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We continue to consider one of the cybernetic methods in computational biology related to the study of DNA chains. Namely, we are considering the problem of reconstructing the not fully filled distance matrix of DNA chains. When applied in a programming context, it is revealed that with a modern computer of average capabilities, creating even a small-sized distance matrix for mitochondrial DNA sequences is quite time-consuming with standard algorithms. As the size of the matrix grows larger, the computational effort required increases significantly, potentially spanning several weeks to months of non-stop computer processing. Hence, calculating the distance matrix on conventional computers is hardly feasible, and supercomputers are usually not available. Therefore, we started publishing our variants of the algorithms for calculating the distance between two DNA chains; then, we published algorithms for restoring partially filled matrices, i.e., the inverse problem of matrix processing. In this paper, we propose an algorithm for restoring the distance matrix for DNA chains, and the primary focus is on enhancing the algorithms that shape the greedy function within the branches and boundaries method framework.

Keywords: DNA chains, distance matrix, optimization problem, restoring algorithm, greedy algorithm, heuristics

Procedia PDF Downloads 111

Authors: Tegan H. Emerson, Colin C. Olson, George Stantchev, Jason A. Edelberg, Michael Wilson

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Detecting small targets at range is difficult because there is not enough spatial information present in an image sub-region containing the target to use correlation-based methods to differentiate it from dynamic confusers present in the scene. Moreover, this lack of spatial information also disqualifies the use of most state-of-the-art deep learning image-based classifiers. Here, we use characteristics of target tracks extracted from video sequences as data from which to derive distinguishing topological features that help robustly differentiate targets of interest from confusers. In particular, we calculate persistent homology from time-delayed embeddings of dynamic statistics calculated from motion tracks extracted from a wide field-of-view video stream. In short, we use topological methods to extract features related to target motion dynamics that are useful for classification and disambiguation and show that small targets can be detected at range with high probability.

Keywords: motion tracks, persistence images, time-delay embedding, topological data analysis

Procedia PDF Downloads 108